Description

Clips read alignments where they match BED file defined regions

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bed{:bash}

:file

BED file of regions to be removed (e.g. amplicon primers)

*.{bed}

save_cliprejects{:bash}

:boolean

Save filtered reads to a file

save_clipstats{:bash}

:boolean

Save clipping stats to a file

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.clipallowed.bam{:bash}

:file

Clipped reads BAM file

*.{bam}

stats{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.clipstats.txt{:bash}

:file

Clipping statistics text file

*.{clipstats.txt}

rejects_bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.cliprejects.bam{:bash}

:file

Filtered reads BAM file

*.{cliprejects.bam}

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
maintainers
Github user bjohnnyd
Github user matthdsm
get in touch
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